99,549 research outputs found
ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality
Summary: The ModuLand plug-in provides Cytoscape users an algorithm for
determining extensively overlapping network modules. Moreover, it identifies
several hierarchical layers of modules, where meta-nodes of the higher
hierarchical layer represent modules of the lower layer. The tool assigns
module cores, which predict the function of the whole module, and determines
key nodes bridging two or multiple modules. The plug-in has a detailed
JAVA-based graphical interface with various colouring options. The ModuLand
tool can run on Windows, Linux, or Mac OS. We demonstrate its use on protein
structure and metabolic networks. Availability: The plug-in and its user guide
can be downloaded freely from: http://www.linkgroup.hu/modules.php. Contact:
[email protected] Supplementary information: Supplementary
information is available at Bioinformatics online.Comment: 39 pages, 1 figure and a Supplement with 9 figures and 10 table
Robustness and modular structure in networks
Complex networks have recently attracted much interest due to their
prevalence in nature and our daily lives [1, 2]. A critical property of a
network is its resilience to random breakdown and failure [3-6], typically
studied as a percolation problem [7-9] or by modeling cascading failures
[10-12]. Many complex systems, from power grids and the Internet to the brain
and society [13-15], can be modeled using modular networks comprised of small,
densely connected groups of nodes [16, 17]. These modules often overlap, with
network elements belonging to multiple modules [18, 19]. Yet existing work on
robustness has not considered the role of overlapping, modular structure. Here
we study the robustness of these systems to the failure of elements. We show
analytically and empirically that it is possible for the modules themselves to
become uncoupled or non-overlapping well before the network disintegrates. If
overlapping modular organization plays a role in overall functionality,
networks may be far more vulnerable than predicted by conventional percolation
theory.Comment: 14 pages, 9 figure
eXamine: a Cytoscape app for exploring annotated modules in networks
Background. Biological networks have growing importance for the
interpretation of high-throughput "omics" data. Statistical and combinatorial
methods allow to obtain mechanistic insights through the extraction of smaller
subnetwork modules. Further enrichment analyses provide set-based annotations
of these modules.
Results. We present eXamine, a set-oriented visual analysis approach for
annotated modules that displays set membership as contours on top of a
node-link layout. Our approach extends upon Self Organizing Maps to
simultaneously lay out nodes, links, and set contours.
Conclusions. We implemented eXamine as a freely available Cytoscape app.
Using eXamine we study a module that is activated by the virally-encoded
G-protein coupled receptor US28 and formulate a novel hypothesis about its
functioning
Self-organized learning in multi-layer networks
We present a framework for the self-organized formation of high level learning by a statistical preprocessing of features. The paper focuses first on the formation of the features in the context of layers of feature processing units as a kind of resource-restricted associative multiresolution learning We clame that such an architecture must reach maturity by basic statistical proportions, optimizing the information processing capabilities of each layer. The final symbolic output is learned by pure association of features of different levels and kind of sensorial input. Finally, we also show that common error-correction learning for motor skills can be accomplished also by non-specific associative learning. Keywords: feedforward network layers, maximal information gain, restricted Hebbian learning, cellular neural nets, evolutionary associative learnin
On combinatorial optimisation in analysis of protein-protein interaction and protein folding networks
Abstract: Protein-protein interaction networks and protein folding networks represent prominent research topics at the intersection of bioinformatics and network science. In this paper, we present a study of these networks from combinatorial optimisation point of view. Using a combination of classical heuristics and stochastic optimisation techniques, we were able to identify several interesting combinatorial properties of biological networks of the COSIN project. We obtained optimal or near-optimal solutions to maximum clique and chromatic number problems for these networks. We also explore patterns of both non-overlapping and overlapping cliques in these networks. Optimal or near-optimal solutions to partitioning of these networks into non-overlapping cliques and to maximum independent set problem were discovered. Maximal cliques are explored by enumerative techniques. Domination in these networks is briefly studied, too. Applications and extensions of our findings are discussed
Tiling solutions for optimal biological sensing
Biological systems, from cells to organisms, must respond to the ever
changing environment in order to survive and function. This is not a simple
task given the often random nature of the signals they receive, as well as the
intrinsically stochastic, many body and often self-organized nature of the
processes that control their sensing and response and limited resources.
Despite a wide range of scales and functions that can be observed in the living
world, some common principles that govern the behavior of biological systems
emerge. Here I review two examples of very different biological problems:
information transmission in gene regulatory networks and diversity of adaptive
immune receptor repertoires that protect us from pathogens. I discuss the
trade-offs that physical laws impose on these systems and show that the optimal
designs of both immune repertoires and gene regulatory networks display similar
discrete tiling structures. These solutions rely on locally non-overlapping
placements of the responding elements (genes and receptors) that, overall,
cover space nearly uniformly.Comment: 11 page
Nonlinear Hebbian learning as a unifying principle in receptive field formation
The development of sensory receptive fields has been modeled in the past by a
variety of models including normative models such as sparse coding or
independent component analysis and bottom-up models such as spike-timing
dependent plasticity or the Bienenstock-Cooper-Munro model of synaptic
plasticity. Here we show that the above variety of approaches can all be
unified into a single common principle, namely Nonlinear Hebbian Learning. When
Nonlinear Hebbian Learning is applied to natural images, receptive field shapes
were strongly constrained by the input statistics and preprocessing, but
exhibited only modest variation across different choices of nonlinearities in
neuron models or synaptic plasticity rules. Neither overcompleteness nor sparse
network activity are necessary for the development of localized receptive
fields. The analysis of alternative sensory modalities such as auditory models
or V2 development lead to the same conclusions. In all examples, receptive
fields can be predicted a priori by reformulating an abstract model as
nonlinear Hebbian learning. Thus nonlinear Hebbian learning and natural
statistics can account for many aspects of receptive field formation across
models and sensory modalities
Pre-integration lateral inhibition enhances unsupervised learning
A large and influential class of neural network architectures use
post-integration lateral inhibition as a mechanism for competition. We argue
that these algorithms are computationally deficient in that they fail to
generate, or learn, appropriate perceptual representations under certain
circumstances. An alternative neural network architecture is presented in which
nodes compete for the right to receive inputs rather than for the right to
generate outputs. This form of competition, implemented through pre-integration
lateral inhibition, does provide appropriate coding properties and can be used
to efficiently learn such representations. Furthermore, this architecture is
consistent with both neuro-anatomical and neuro-physiological data. We thus
argue that pre-integration lateral inhibition has computational advantages over
conventional neural network architectures while remaining equally biologically
plausible
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